AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ipurR_ecoli_bsub_100.orf -g0.5 -x5 Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 carA 300 carbamoyl-phosphate synthetase, glutamine (small) subunit #2 codB 300 cytosine permease/transport #3 purE 117 phosphoribosylaminoimidazole carboxylase = AIR carboxylase, catalytic subunit #4 pyrD 110 dihydro-orotate dehydrogenase #5 pyrC 105 dihydro-orotase #6 ycfC 35 orf, hypothetical protein #7 ymfC 201 orf, hypothetical protein #8 prsA 150 phosphoribosylpyrophosphate synthetase #9 purR 300 transcriptional repressor for pur regulon, glyA, glnB, prsA, speA #10 purT 133 phosphoribosylglycinamide formyltransferase 2 #11 ubiX 94 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #12 purF 36 amidophosphoribosyltransferase = PRPP amidotransferase #13 cvpA 258 membrane protein required for colicin V production #14 purC 212 phosphoribosylaminoimidazole-succinocarboxamide synthetase = SAICAR synthetase #15 purM 297 phosphoribosylaminoimidazole synthetase = AIR synthetase #16 guaA 68 GMP synthetase (glutamine-hydrolyzing) #17 guaB 161 IMP dehydrogenase #18 glyA 300 serine hydroxymethyltransferase #19 glnB 60 regulatory protein P-II for glutamine synthetase #20 yfhG 164 putative alpha helix protein #21 purL 300 phosphoribosylformyl-glycineamide synthetase = FGAM synthetase #22 gcvP 118 glycine decarboxylase, P protein of glycine cleavage system #23 gcvH 23 in glycine cleavage complex, carrier of aminomethyl moiety via covalently bound lipoyl cofactor #24 gcvT 300 aminomethyltransferase (T protein; tetrahydrofolate-dependent) of glycine cleavage system #25 yqgB 120 orf, hypothetical protein #26 purH 300 phosphoribosylaminoimidazolecarboxamideformyltransferase = AICAR formyltransferase; IMP cyclohydrolase #27 purA 103 adenylosuccinate synthetase #28 guaB 120 inositol-monophosphate dehydrogenase #29 gcaD 192 UDP-N-acetylglucosamine pyrophosphorylase #30 prs 22 phosphoribosyl pyrophosphate synthetase #31 purT 230 phosphoribosylglycinamide formyltransferase 2 #32 yclB 89 similar to phenylacrylic acid decarboxylase #33 guaA 232 GMP synthetase #34 purE 300 phosphoribosylaminoimidazole carboxylase I #35 purC 72 phosphoribosylaminoimidazole succinocarboxamide synthetase #36 purM 101 phosphoribosylaminoimidazole synthetase #37 yhjM 103 similar to transcriptional regulator (LacI family) #38 yisR 123 alternate gene name: yuxC, yucF; similar to transcriptional regulator (AraC/XylS family) #39 argC 206 N-acetylglutamate gamma-semialdehyde dehydrogenase #40 carA 70 carbamoyl-phosphate transferase-arginine (subunit A) #41 yjmC 104 similar to malate dehydrogenase #42 yjmE 24 similar to D-mannonate hydrolase #43 yjmG 47 similar to hexuronate transporter #44 yjmH 87 similar to transcriptional regulator (LacI family) #45 pyrB 145 aspartate carbamoyltransferase #46 yqhJ 29 similar to glycine dehydrogenase #47 yqhI 300 similar to aminomethyltransferase #48 ccpA 274 transcriptional regulator (Lacl family) #49 yusH 66 similar to glycine cleavage system protein H #50 yusI 110 similar to arsenate reductase #51 rbsR 300 transcriptional regulator (LacI family) #52 nrgA 281 ammonium transporter #53 glyA 206 serine hydroxymethyltransferase #54 purA 205 adenylosuccinate synthetase Motif number 1 TTCTTGCTGCGCAAGCGTTTTCCAGAACAGGT 1 67 1 GCAACGTTTC 0.837032 -234 AAGATAAAAAGCAATCGTTTTCGTGGGGAAAT 2 221 0 GCAACGTTTC 0.837032 -80 TCACAGCCACGCAACCGTTTTCCTTGCTCTCT 3 33 1 GCAACGTTTC 0.576495 -85 CAAAAAAAACGCAAACGTTTTCCGAACCTGTT 4 11 0 GCAACGTTTC 0.518164 -100 TCGTGCAAAGGAAAACGTTTCCGCTTATCCTT 5 41 1 GAAACGTTTC 0.543511 -65 GTGTGTAAAGGCAAACGTTTACCTTGCGATTT 9 243 1 GCAACGTTTC 0.504824 -58 AAAGACACACGCAAACGTTTTCGTTTATACTG 10 83 1 GCAACGTTTC 0.518164 -51 AAATCCCTACGCAAACGTTTTCTTTTTCTGTT 13 189 1 GCAACGTTTC 0.518164 -70 GATATGATACGCAAACGTGTGCGTCTGCAGGA 14 46 1 GCAACGTGTC 0.545119 -167 AACAGGGAAAGCAAACGTTTGCGAGACTGCTT 15 221 0 GCAACGTTTC 0.499988 -77 AGGGGTAGATGCAATCGGTTACGCTCTGTATA 17 95 1 GCAACGGTTC 0.683939 -67 TAGCCTGAAGGTAATCGTTTGCGTAAATTCCT 18 169 1 GTAACGTTTC 0.548953 -132 TTATTTCCACGCAAACGGTTTCGTCAGCGCAT 21 211 1 GCAACGGTTC 0.513138 -90 GGTCCCCAACGCAATCGTTCTCTTTTGCCTGA 24 197 0 GCAACGTTCC 0.953859 -104 CGAGCGTTGCGCAAACGTTTTCGTTACAATGC 26 180 1 GCAACGTTTC 0.518164 -121 TAAAAACCAAGTATACGTTTTCATCATCTATA 48 71 1 GTATCGTTTC 0.643789 -204 CCTTGTTTATGTAACCGTTTACATAGATAGAT 51 269 0 GTAACGTTTC 0.519388 -32 CATTCGTTTTATAAGCGTTTTCTCACTGCTTT 54 57 0 ATAACGTTTC 0.651661 -149 **** ***** * Masking position 3 Map Score: 56.1507 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 6 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 2 AACGCGTCAGCGTCGCATCAGGCATCGGCACAC 2 19 0 CGTCCATCGC 0.986719 -282 GCGACGCGAGCGCCTTATCCGACCTACGGTTCA 2 70 0 CGCCTATCGC 0.993383 -231 AAGGCGCTCGCGTCGCATCCGACACCATGCTCA 2 87 1 CGTCCATCGC 0.986719 -214 GACGCGTCAGCGTCGCATCAGGCATCTGAGCAT 2 113 0 CGTCCATCGC 0.986719 -188 GACGCTGACGCGTCTTATCAGGCCTACCCACTG 2 132 1 CGTCTATCGC 0.988124 -169 AAATAGTTGCCCTGTCAGACTTGCAGGCAG 11 75 0 TGCCTGTCGC 0.730308 -20 GACGCGCCAGCGTCGCATCAGGCAAGACCGTA 13 10 0 CGTCCATCGC 0.986719 -249 GACGCTGGCGCGTCTTATCAGGCCTACGCAGGG 13 29 1 CGTCTATCGC 0.988124 -230 GCGGCGTAAACGCCTTATCCGACCTACGGTTCT 13 64 0 CGCCTATCGC 0.993383 -195 AAGGCGTTTACGCCGCATCCGACACGCATTGCC 13 81 1 CGCCCATCGC 0.992596 -178 CACGATTTTACGCCCTGTCATCCTGTTCGGGGC 13 228 0 CGCCTGTCTC 0.886448 -31 GCGGCGTGAACGCCTTATCCGAACTACGTCCGA 14 117 0 CGCCTATCGA 0.88159 -96 AAGGCGTTCACGCCGCATCCGACAAAACATCCG 14 134 1 CGCCCATCGC 0.992596 -79 CTTCGCCCGACTTCATGTCGGGCGATTTATATT 16 15 1 CTTCTGTCGC 0.858371 -54 AAGAAAGCGCCTCCTTATCATACCTTTTAGGTA 32 11 1 CTCCTATCTC 0.81127 -79 GCGGAGCGAGCTTCATATCTGTCCTCGTTTTTT 33 172 1 CTTCTATCGC 0.943386 -61 GTCTCATTCCTCCGTATCTTTCAGAATAAAAA 52 260 0 CTCCTATCTC 0.81127 -22 **** **** * * Masking position 8 Map Score: 38.718 Number of sites scoring better than the average of aligned sites = 939 Number in coding regions = 238 Number in noncoding regions = 701 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 3 GCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAG 1 61 1 TGCTCGCGTT 0.971671 -240 CGATGCCTGATGCGACGCTGACGCGTTTTATCATGC 2 25 1 TGCGCGCGCT 0.997644 -276 TGGTGTCGGATGCGACGCGAGCGCCTTATCCGACCT 2 78 0 TGCGCGCGCT 0.997644 -223 AGATGCCTGATGCGACGCTGACGCGTCTTATCAGGC 2 119 1 TGCGCGCGCT 0.997644 -182 TCTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGC 13 16 1 TGCGCGCGCT 0.997644 -243 GCGTGTCGGATGCGGCGTAAACGCCTTATCCGACCT 13 72 0 TGCGCGCGCT 0.997644 -187 TTTTCTGATATGATACGCAAACGTGTGCGTCTGCAG 14 40 1 TGATCGCGTT 0.894693 -173 TTTTGTCGGATGCGGCGTGAACGCCTTATCCGAACT 14 125 0 TGCGCGCGCT 0.997644 -88 CTAAAAGGTATGATAAGGAGGCGCTTTCTT 32 5 0 TGATAGCGCT 0.812919 -85 ACAAAAACGTTGATGCGGTGCCGCATTTCAGCCGCA 39 32 0 TGATCGCGCT 0.98219 -175 CTCCGCAGTTTGCTCCTTCGGCGCCTGTATCCCGAG 47 70 0 TGCTCTCGCT 0.946069 -231 **** ** *** * Masking position 1 Map Score: 22.8234 Number of sites scoring better than the average of aligned sites = 337 Number in coding regions = 66 Number in noncoding regions = 271 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 4 GTTCTGGAAAACGCTTGCGCAGCAAGAAGATTG 1 62 0 ACGCGCGAGC 0.864071 -239 ATGATAAAACGCGTCAGCGTCGCATCAGGCATC 2 26 0 GCGTGCGCGC 0.976857 -275 GTCGGATAAGGCGCTCGCGTCGCATCCGACACC 2 80 1 GCGCGCGCGC 0.997557 -221 CTGATAAGACGCGTCAGCGTCGCATCAGGCATC 2 120 0 GCGTGCGCGC 0.976857 -181 AATAAAGGGCGCGAATGCGCCCTCGTGA 5 6 0 GCGAGCGCCT 0.778944 -100 CGTTGCATATGCGTTTGCGTCCTGCGATACGGA 7 54 1 GCGTGCGCCT 0.944361 -148 CTGATAAGACGCGCCAGCGTCGCATCAGGCAAG 13 17 0 GCGCGCGCGC 0.977562 -242 GTCGGATAAGGCGTTTACGCCGCATCCGACACG 13 74 1 GCGTACGCGC 0.979882 -185 TTCGGATAAGGCGTTCACGCCGCATCCGACAAA 14 127 1 GCGTACGCGC 0.979882 -86 ATTCTCTGTGTCGTGCGCGTCCCAGCTTGAAAA 21 61 1 TCGTGCGCCC 0.949546 -240 AGAGAAAAATTCGCGAGCGTTGCGCAAACGTTT 26 167 1 TCGCGCGTGC 0.864071 -134 AAAGAGCTCCGCGCATGCGGAGCTCATGGCCAA 50 11 0 GCGCGCGAGC 0.98641 -100 **** *** *** Masking position 8 Map Score: 20.04 Number of sites scoring better than the average of aligned sites = 666 Number in coding regions = 549 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 5 TCAACTTAATGGCGGGATTTTTTATATTATTT 1 148 0 GGCGGTTTTT 0.98163 -153 TCTGGCAAACGGCGGCATTCTGGAGATATGGG 1 189 0 GGCGGTTCTG 0.85364 -112 AATAGAATGCGGCGGATTTTTTGGGTTTCAAA 2 259 1 GGCGGTTTTT 0.98163 -42 GCCGGGCAAGCTGAGTTTCGGTGACAACGT 8 9 1 AGCTGTTTCG 0.849172 -142 ACGCGATTTTAGCGGTAATTCGCACGAAATTT 14 80 1 AGCGGATTCG 0.642629 -133 TGAAAAGGTCGCCTGTCTTTTGATCTGCTAAA 19 30 0 GCCTGTTTTG 0.818104 -31 CTCATAAATGAGCGGCATTTTGCGTAAACCTG 21 118 1 AGCGGTTTTG 0.969833 -183 GTGGCTCCGATGCTGGGTTTCGTGGTGATAAT 24 233 1 TGCTGTTTCG 0.691601 -68 AAAGGTATAAAGCGGGCTTTTGCTGGGGAATG 26 49 0 AGCGGTTTTG 0.969833 -252 TAGGGGCGTTAGCTGAGTTTTTCGCGAAAAAT 26 236 1 AGCTGTTTTT 0.925228 -65 AGAGAGCGTTAGCTGAATTTTTCGCGAAAAAC 26 252 0 AGCTGTTTTT 0.925228 -49 GCCTTTTGCCGGCGGTCCTTTTTTAATTCTGA 29 53 1 GGCGGCTTTT 0.857017 -140 TGCAATGCAGAGCGGGTATTTTTTATTTTCTG 34 248 1 AGCGGATTTT 0.798069 -53 AGCGCAGTTCGGCTGCCTTTCTCTTTCTGCCC 36 34 1 GGCTGTTTCT 0.90346 -68 CGCGGTCAGCCTGTTTTTTTATGCGGCTGA 39 9 1 GCCTGTTTTT 0.805574 -198 GCTGGAGTCGTGCTGATTTTTTTTGAGCGGAA 39 68 1 TGCTGTTTTT 0.831331 -139 TAGTGGGAGAGGCGGTATGTTTGATGATACAA 44 21 1 GGCGGTGTTT 0.843089 -67 TCTATCTTAGACCGGGGTTTTTTTTCAGCCTT 45 99 1 ACCGGTTTTT 0.846057 -47 AAGGCCGCACGGCGGCCTTTTGGATTGTTCAA 48 11 0 GGCGGTTTTG 0.983053 -264 AAGGCCGCCGTGCGGCCTTTTTTTATGCTTTC 48 24 1 TGCGGTTTTT 0.921853 -251 ***** ***** Masking position 5 Map Score: 17.0869 Number of sites scoring better than the average of aligned sites = 993 Number in coding regions = 813 Number in noncoding regions = 180 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 6 TTGCTGCGCAAGCGTTTTCCAGAACAGGTTA 1 70 1 ACGTTTTCCA 0.748714 -231 ATAAAAAGCAATCGTTTTCGTGGGGAAATAT 2 219 0 ACGTTTTCGT 0.980163 -82 CAGCCACGCAACCGTTTTCCTTGCTCTCTTT 3 36 1 ACGTTTTCCT 0.954622 -82 AGGTTCGGAAAACGTTTGCGTTTTTTTTGCC 4 14 1 ACGTTTGCGT 0.989986 -97 GATAAGCGGAAACGTTTTCCTTTGCACGAAA 5 39 0 ACGTTTTCCT 0.954622 -67 ACGTTGCATATGCGTTTGCGTCCTGCGATAC 7 53 1 TCGTTTGCGT 0.888144 -149 TCGCAAGGTAAACGTTTGCCTTTACACACCT 9 241 0 ACGTTTGCCT 0.976792 -60 GACACACGCAAACGTTTTCGTTTATACTGCG 10 86 1 ACGTTTTCGT 0.980163 -48 AGAAAAAGAAAACGTTTGCGTAGGGATTTCC 13 187 0 ACGTTTGCGT 0.989986 -72 ATGATACGCAAACGTGTGCGTCTGCAGGAAA 14 49 1 ACGTGTGCGT 0.917275 -164 CCGCTAAAATCGCGTTTTCCTGCAGACGCAC 14 64 0 CCGTTTTCCT 0.714638 -149 AGGGAAAGCAAACGTTTGCGAGACTGCTTTA 15 219 0 ACGTTTGCGA 0.933339 -79 CCTGAAGGTAATCGTTTGCGTAAATTCCTTT 18 172 1 ACGTTTGCGT 0.989986 -129 CGCTGACGAAACCGTTTGCGTGGAAATAAAA 21 209 0 ACGTTTGCGT 0.989986 -92 GGCAAAAGAGAACGATTGCGTTGGGGACCGG 24 200 1 ACGATTGCGT 0.882095 -101 GCGTTGCGCAAACGTTTTCGTTACAATGCGG 26 183 1 ACGTTTTCGT 0.980163 -118 TTTCAAAATCACCGTTTGCTTAAAAATGGAT 27 82 0 ACGTTTGCTT 0.866867 -22 GCACCGCATCAACGTTTTTGTGCTGGAGTCG 39 47 1 ACGTTTTTGT 0.697692 -160 * ********* Masking position 7 Map Score: 36.8586 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 41 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 7 AAACGAGCAGAAAAAAGTGGACCAAATGGTC 1 21 0 AAAAAAGGGA 0.703939 -280 TGAGTGCAAAAAGGTGGGGGAAAAATTATCG 2 174 0 AAGGTGGGGA 0.88563 -127 TCAAACAGCAAAAAGGGGGAATTTC 2 286 1 AAAAGGGGAA 0.925609 -15 ACGAAAAATAAAGGGCGCGAATGCGCCCTCG 5 14 0 AAGGGCGGAA 0.875196 -92 TGTGGTAATAAAAAAGGAGAAAACTTGAT 9 9 0 AAAAAGGGAA 0.845457 -292 CGGTGTACCCAAGGGGGGGAAACGGGCGTCA 21 257 0 AAGGGGGGAA 0.972849 -44 ATTTTGCCGAAAAGAGGGGGATTTACTA 28 103 1 AAAGAGGGGA 0.905449 -18 GGCCTTGCCAAAGAGGGCGGAGCGAGCTTCA 33 156 1 AAGAGGGGGA 0.960191 -77 TGACACAGAAAAAAACGAGGACAGATATGAA 33 183 0 AAAAACGGGA 0.537513 -50 AAAGCATTAGAAGGTGGGGAACAGA 34 286 1 AAGGTGGGAA 0.877053 -15 AAAGCGCCTTAAAGGAGTGAATAGG 36 87 1 AAAGGAGGAA 0.889302 -15 CAACTTTTTTAAGGAAGGGAAAAT 37 90 1 AAGGAAGGAA 0.863159 -14 AATCCGACTTAAAAAGGAGGATGATTCAA 38 105 1 AAAAAGGGGA 0.855876 -19 CACAAAGACCAAGAGGGTGAACTTGTT 39 190 1 AAGAGGGGAA 0.956933 -17 CCGGTATGATAAGGAAGGGAATTAG 44 73 1 AAGGAAGGAA 0.863159 -15 TTAAGTTGAAAAGAGAGGGGAAAGAAC 45 129 1 AAGAGAGGGA 0.906167 -17 CGCCGTTGATAAAGGGGAGGAATTAG 47 285 1 AAAGGGGGGA 0.956102 -16 TAGACCTGTAAATGGGGAGAAACAGAAAAGA 51 59 0 AATGGGGGAA 0.738443 -242 CTTTGTCAAAAAAAGAGTGAAAACCTTAAAT 51 163 1 AAAAGAGGAA 0.832826 -138 CTTTTATTTTAAGATAGTGAAATAAATTCCG 53 34 1 AAGATAGGAA 0.639143 -173 ******* *** Masking position 2 Map Score: 18.6964 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 318 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 8 AATTGACCTGCGGCAAAAAAAACGCAAACGT 4 25 0 CGCAAAAAAA 0.74809 -86 GATTTCTCAACCGAAAAGAAATATACTGTAT 10 40 0 CGAAAAGAAA 0.74809 -94 GATGCCGCAAAGGCATAAAAAGTCGATGGCG 13 115 1 AGCATAAAAA 0.806813 -144 CTTCCCGCGCATCAATAAAAATGGCGCTGAA 13 157 0 ACAATAAAAA 0.799024 -102 CATCACAAACCTGAAAAGAAATCCGTTTCCG 18 106 1 CGAAAAGAAA 0.74809 -195 AAAATCGCGACAGAATAAAAAACCAAAAAAT 24 93 0 CGAATAAAAA 0.905145 -208 CCGCAATAGAAAAATTGCAGAA 26 2 1 CCAATAGAAA 0.818997 -299 CTTAGTTGCACTCAATAGAAAATTCTTGCAC 29 94 1 CCAATAGAAA 0.818997 -99 TATCCCTTTTATCCATAGAAAAATATATCCT 29 158 0 ACCATAGAAA 0.664465 -35 CGCATTTCAGCCGCATAAAAAAACAGGCTGA 39 16 0 CGCATAAAAA 0.870712 -191 GGGAATTCCGCTCAAAAAAAATCAGCACGAC 39 74 0 CCAAAAAAAA 0.7387 -133 AAATTTATAAATGAATAAAAATATTAAATAT 39 115 1 AGAATAAAAA 0.855438 -92 ACATTATAACATGAATAAAAATTAATTCAAT 39 149 0 AGAATAAAAA 0.855438 -58 TTCGATATAAAGGCATAAAAATTCATTTTTA 40 17 1 AGCATAAAAA 0.806813 -54 CAACTTAAGGCTGAAAAAAAACCCCGGTCTA 45 106 0 CGAAAAAAAA 0.807978 -40 ATAAACGAGAAAGCATAAAAAAAGGCCGCAC 48 33 0 AGCATAAAAA 0.806813 -242 CAATAAAAATATCAAAAGAAATCTAATTGTA 51 215 0 ACAAAAGAAA 0.553026 -86 ATCCGAAGTTAGCAATAAAAATATCAAAAGA 51 227 0 ACAATAAAAA 0.799024 -74 CCGTATCTTTCAGAATAAAAAGCAATTATTA 52 250 0 CGAATAAAAA 0.905145 -32 ATTCGTTTTTACCAATAAAAATTTAGATTTT 53 93 1 ACAATAAAAA 0.799024 -114 * ********* Masking position 5 Map Score: 16.9031 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 132 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 9 GCTGCGCAAGCGTTTTCCAGAACAGGTTAG 1 72 1 CGTTTTCCAG 0.72908 -229 AGAATGCCGCCGTTTGCCAGAAATTCGTCG 1 200 1 CGTTTGCCAG 0.951338 -101 GTTTGCGTTTTTTTTGCCGCAGGTCAATTC 4 27 1 TTTTTGCCGC 0.34462 -84 TGAAGGGATGTTTTTGCCGGACACAAAGGA 5 68 0 TTTTTGCCGG 0.899209 -38 ACTACCCTATTGTTTGCCGTCATGAAAGAT 7 134 1 TGTTTGCCGT 0.523845 -68 ACAACGTCACCTTGTTCCAGACGTTGCATC 8 34 1 CTTGTTCCAG 0.3514 -117 GCTCCGTGTCGTTTTTCCGGCGTACCGCAA 9 194 1 GTTTTTCCGG 0.546228 -107 GCAAGGTAAACGTTTGCCTTTACACACCTT 9 240 0 CGTTTGCCTT 0.619639 -61 TAAACGAAAACGTTTGCGTGTGTCTTTATT 10 80 0 CGTTTGCGTG 0.802921 -54 GCTAAAATCGCGTTTTCCTGCAGACGCACA 14 63 0 CGTTTTCCTG 0.761788 -150 GCACGAAATTTGTTTGTCGGACGTAGTTCG 14 101 1 TGTTTGTCGG 0.511775 -112 TGTGCCGGATGTTTTGTCGGATGCGGCGTG 14 142 0 GTTTTGTCGG 0.368795 -71 TTTGCTGTCTGGTGTGCCGGATGTTTTGTC 14 154 0 GGTGTGCCGG 0.844821 -59 CGAAAGAAGACTTGTGCCAGGGTAAAGGTT 15 152 0 CTTGTGCCAG 0.797398 -146 GGAAAGCAAACGTTTGCGAGACTGCTTTAC 15 218 0 CGTTTGCGAG 0.774188 -80 CTGACGAAACCGTTTGCGTGGAAATAAAAT 21 208 0 CGTTTGCGTG 0.802921 -93 CAATCGTTCTCTTTTGCCTGAACTTACCAC 24 188 0 CTTTTGCCTG 0.929631 -113 ATAAAGCGGGCTTTTGCTGGGGAATGCAGC 26 45 0 CTTTTGCTGG 0.764207 -256 TGACATAAGCCTTTTGCCGGCGGTCCTTTT 29 45 1 CTTTTGCCGG 0.976548 -148 TTGGCAAGGCCGTTTGCCGGAGTCAGGCCA 33 137 0 CGTTTGCCGG 0.986527 -96 CGGCAATTTACGGTTGCCGGGTAGAAACTT 34 115 0 CGGTTGCCGG 0.864362 -186 CATCAACGTTTTTGTGCTGGAGTCGTGCTG 39 53 1 TTTGTGCTGG 0.197327 -154 AGCAAGAGTTCTTTTGCCTGAGAGATTCAC 47 105 0 CTTTTGCCTG 0.929631 -196 ********** Masking position 5 Map Score: 15.0653 Number of sites scoring better than the average of aligned sites = 2125 Number in coding regions = 1968 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 10 CGTTTTCCTTGCTCTCTTTCCGTGCTATTC 3 48 1 GCTCTCTTTC 0.650095 -70 ACGCAAACGTTTTCTTTTTCTGTTAGAATG 13 197 1 TTTCTTTTTC 0.68363 -62 CGATTTATATTATCTGTTTCACTTGCCTCG 16 37 1 TATCTGTTTC 0.700966 -32 ATTAGTTAATTCTCTGTGTCGTGCGCGTCC 21 53 1 TCTCTGTGTC 0.840253 -248 CTCGCGAATTTTTCTCTTTCAATGGTGATC 26 154 0 TTTCTCTTTC 0.93319 -147 TCCTCGTTTTTTTCTGTGTCAAAAAACTTA 33 193 1 TTTCTGTGTC 0.931995 -40 TTCGGCTGCCTTTCTCTTTCTGCCCTCGTT 36 41 1 TTTCTCTTTC 0.93319 -61 GTTGGTTCAGTTTCTGTTGCACCGCTTTCG 43 11 0 TTTCTGTTGC 0.740924 -37 TAAAATGAAGGTTCTCTGTCCTGGCACCTG 47 213 0 GTTCTCTGTC 0.799294 -88 ACATGAGGTGTTTCTCTGTCCTTTTTTGTA 47 242 1 TTTCTCTGTC 0.919941 -59 ATGATAGTCTTTTCTGTTTCTCCCCATTTA 51 52 1 TTTCTGTTTC 0.943372 -249 TACAATTGACTTTCTGTTTCTTCACTGATA 54 132 1 TTTCTGTTTC 0.943372 -74 ********** Masking position 5 Map Score: 9.34118 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 86 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 11 TAGCGCTCGAAGGAGAGGTGA 7 2 0 AGGAGAGGTG 0.827677 -200 ATAGCCTGATAGGATAGGCTGTTAGCA 20 8 0 AGGATAGGCT 0.675284 -157 TACGCCCACTGGGATAGGCTTTAAGTCTGG 20 140 1 GGGATAGGCT 0.889161 -25 CCTCTTCTGCGGGAGAGGATCAGGGTGAGG 22 21 1 GGGAGAGGAT 0.965214 -98 GAGAGGATCAGGGTGAGGAAAATTTATGCC 22 33 1 GGGTGAGGAA 0.763279 -86 AAGAGAGTGAGGGTGAGGCATAAATTTTCC 22 49 0 GGGTGAGGCA 0.837185 -70 TCTTCGTAAGGAGAGAGGTTCACAATTCAC 22 75 1 GAGAGAGGTT 0.723434 -44 GTTGGGGACCGGGAGTGGCTCCGATGCTGG 24 219 1 GGGAGTGGCT 0.892512 -82 CCCAACATTCGGGTTAGGAGGCCTTCC 35 56 1 GGGTTAGGAG 0.6337 -17 ACCAACATAGGGGTGAGGTTGAG 43 35 1 GGGTGAGGTT 0.903984 -13 GAAATATAGTGGGAGAGGCGGTATGTTTGA 44 15 1 GGGAGAGGCG 0.973263 -73 TTTTTTCTTGGAGAGAGGAGACAACAC 46 13 1 GAGAGAGGAG 0.726116 -17 ATCCAGTAAAAGGAGTGGTTTTAGG 48 260 1 AGGAGTGGTT 0.522808 -15 GGATACGGATAGGAGAGGATCTCGCTG 53 190 1 AGGAGAGGAT 0.877945 -17 ********** Masking position 7 Map Score: 7.90365 Number of sites scoring better than the average of aligned sites = 335 Number in coding regions = 230 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 12 GAAATTCCCCCTTTTTGCTGTTTGAAA 2 284 0 TCCCCTTTTG 0.673362 -17 GTTCACTGCTTCCTTGTTTTAAGTA 6 21 0 TCTGCTTCTT 0.875181 -15 ATCAAGTTTTCTCCTTTTTTATTACCACAC 9 8 1 TCTCCTTTTT 0.672913 -293 TTTTTACCACTTCCCCTTTTCGTCAAGATCGGC 9 109 1 TCCCTTTCGT 0.718587 -192 TACTGGCCATTGACCCCTTCCTGACGCTCCGTG 9 169 1 TCCCCTTCTG 0.956743 -132 CGACGGATTATACCTCCTTTCTTCAAGGCGGCA 15 20 1 TCTCCTTCTT 0.956658 -278 ATTGTGAACCTCTCTCCTTACGAAGAGAGTGAG 22 68 0 TCTCCTTCGA 0.617703 -51 TTTTCAAAATCACCGTTTGCTTAAAAATGGAT 27 82 0 TCCGTTTCTT 0.541116 -22 TTTCAACTCTTTCCCGCTTCCTTGACATGCTCT 28 44 1 TCCGCTTCTT 0.926748 -77 GGGATGCCTCCTGTCGGTGTGGTGGTC 31 5 1 TCTCCTGCGG 0.516751 -226 GACCGTTATTTGTCTGCTTTCGTTTAAGAATTT 31 107 1 TCTGCTTCGT 0.828273 -124 ATTTTCCCTTCCTTAAAAAAGTTG 37 90 0 TTCCCTTCTT 0.663876 -14 CGTGTCTAACCCCTTTCGTAAATAAAATC 38 7 1 TCCCCTTCGT 0.964784 -117 GCAAGTGCCTCCTTCCTTTTCAGTTTTT 41 87 0 TCTCCTTCTT 0.956658 -18 GTTCTTTCCCCTCTCTTTTCAACTTAA 45 129 0 TCCCCTCCTT 0.83473 -17 CGGTCAGGTCTCTCCCCTTGCTGTCATTCGCTC 47 32 0 TCCCCTTCTG 0.956743 -269 AAAAAATGCCATTCTCCTTCCTTTCCATCCCTC 52 136 1 ACTCCTTCTT 0.639357 -146 * ****** *** Masking position 8 Map Score: 8.27396 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 260 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 13 ATGCGACGCTGACGCGTTTTATCATGCCTAC 2 34 1 GACGCTTTTA 0.824578 -267 ATGCGACGCTGACGCGTCTTATCAGGCCTAC 2 128 1 GACGCTCTTA 0.81044 -173 CAAAAAATCCGCCGCATTCTATTCATCTGAA 2 251 0 GCCGCTTCTA 0.959688 -50 ATTATGAATTGCCGCATTATAGCCTAATAAC 7 168 0 GCCGCTTATA 0.866565 -34 ATGCGACGCTGGCGCGTCTTATCAGGCCTAC 13 25 1 GGCGCTCTTA 0.949219 -234 AGGCGTTTACGCCGCATCCGACACGCATTGC 13 82 1 GCCGCTCCGA 0.892593 -177 TCCTGTTCGGGGCGCATTCTAACAGAAAAAG 13 210 0 GGCGCTTCTA 0.959688 -49 AGGCGTTCACGCCGCATCCGACAAAACATCC 14 135 1 GCCGCTCCGA 0.892593 -78 TTAGAATTGCGCCGAATTTTATTTTTCTACC 15 251 1 GCCGATTTTA 0.704745 -47 CTTCATGTCGGGCGATTTATATTATCTGTTT 16 25 1 GGCGATTATA 0.429964 -44 CTCGGCGCTTCTCAGGATTCAAGA 25 4 1 GGCGCTCTCA 0.912663 -117 ATGATAAGGAGGCGCTTTCTT 32 1 0 GGCGCTTCTT 0.700874 -89 ACTCCTTTAAGGCGCTTTTCAAAATATCTCC 36 74 0 GGCGCTTTCA 0.91993 -28 TTGATGCGGTGCCGCATTTCAGCCGCATAAA 39 28 0 GCCGCTTTCA 0.91993 -179 ***** ***** Masking position 7 Map Score: 8.72187 Number of sites scoring better than the average of aligned sites = 459 Number in coding regions = 318 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 14 GAGAATTAACTAATTGAAAAAATTAAAGATTAATTATCTG 21 27 0 TTTAAAAAAT 0.899719 -274 CATTAGCTTATGGTTAAAAAATGCAAAAATCGCGACAGAA 24 109 0 TTTAAAAAAT 0.899722 -192 AGAGTTGAAATATTTAGATAACGGAAAGGATTAAGAAATA 28 14 0 TTTAAAAAAA 0.899719 -107 TTGTCTGCTTTCGTTTAAGAATTTAAAAGATTTTAACCCT 31 116 1 TTTAAAAAAA 0.894664 -115 AAATAAATTTTTATTAAAAAAGATAAAATTATTATTGAGG 31 153 0 TTTAAAAAAT 0.899722 -78 CTAATGCTTTTGTTTTCAGAAAATAAAAAATACCCGCTCT 34 256 0 TTTAAAAAAA 0.899594 -45 GTACCTCCAATGATTTTATAATCTAAAAATTTATTACAAA 37 16 1 TTTAAAAAAT 0.899719 -88 GTAATTAAATTTGATGAATAATGAAAAATAATGTACACTA 48 127 1 TATAAAAAAA 0.761333 -148 TAACACAGTTTGTTTTAAAAACCTAAAACAGTGCTTCTTA 50 46 0 TTTAAAAAAA 0.899594 -65 AATTGTAAATTGTATATATAATTGAAAAATTTAAGGTTTT 51 182 0 TATAAAAAAT 0.761333 -119 TATAAGACTTTGTATCTATAAAAGAAACTATTCATATGAG 52 92 0 TATAAAAAAA 0.761333 -190 TAAAAGATTATTTTTAAAAAATCTAAATTTTTATTGGTAA 53 101 0 TTTAAAAAAT 0.899722 -106 * ** * ** *** * Masking position 10 Map Score: 5.40473 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 29 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 15 ACGGACCTGAACCGTAGGTCGGATAAGGCGCT 2 63 1 ACCGTAGTGG 0.938651 -238 TACGGTTCTACCCCTGCGTAGGCCTGATAAGA 13 41 0 CCCCTGGTGG 0.821263 -218 CAGGGGTAGAACCGTAGGTCGGATAAGGCGTT 13 57 1 ACCGTAGTGG 0.938651 -202 GCTTGCTATCCCCGAAGGGCGGGTTACTATCG 17 50 0 CCCGAAGGGG 0.984235 -112 CTTTCGGTGTACCCAAGGGGGGGAAACGGGCG 21 260 0 ACCCAAGGGG 0.953188 -41 ATAACCGAACGTAAGTGTGAAAGTT 25 106 0 ACCGAAGTAG 0.601802 -15 TCAGCTAACGCCCCTAACGGGGCATCCTTATT 26 220 0 CCCCTACGGG 0.776134 -81 AGACCACCACACCGACAGGAGGCATCCC 31 7 0 ACCGACGGGG 0.84185 -224 GGCCTCCTAACCCGAATGTTGGGAATTTTCAA 35 47 0 CCCGAAGTGG 0.978961 -26 AAAATATCTCCCCGAACGAGGGCAGAAAGAGA 36 53 0 CCCGAAGAGG 0.90619 -49 CTCAACCTCACCCCTATGTTGGTTCAGTTTCT 43 26 0 CCCCTAGTGG 0.960611 -22 GCAAAGACGTCCCCAAAGGTGGTTTGCGCATC 47 163 0 CCCCAAGGGG 0.978282 -138 ****** ** ** Masking position 3 Map Score: 9.2375 Number of sites scoring better than the average of aligned sites = 209 Number in coding regions = 157 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097